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The Open Protein Structure Annotation Network
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3hlz

    Table of contents
    1. 1. Protein Summary
    2. 2. Ligand Summary

    Title Crystal structure of BT_1490 (NP_810393.1) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 1.50 A resolution. To be Published
    Site JCSG
    PDB Id 3hlz Target Id 396688
    Molecular Characteristics
    Source Bacteroides thetaiotaomicron vpi-5482
    Alias Ids TPS25959,NP_810393.1, 332848 Molecular Weight 30298.54 Da.
    Residues 268 Isoelectric Point 4.80
    Sequence mqgkkfispgawfsmnypsdwnefedgegsflfynpdvwtgnfrisafkgnasygkdairqelkendsa slvkigtwdcayskemfqeegtyytshlwitgtgniafecsftvpkggsakeaeeviatlearkegeky paelipvrlseiyqinegyewvvstvkqelkkdfqgveedlekiqqvidsgkispkkkdewlaigitvc ailtnevegmewktlidgnrevpvleyqgrtidpmkiawskvkagqpcniaeayqsaidhh
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 1.50 Rfree 0.195
    Matthews' coefficent 2.15 Rfactor 0.169
    Waters 448 Solvent Content 42.80

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3hlz
    1. Structure of the Sensor Domain of Mycobacterium tuberculosis PknH Receptor Kinase Reveals a Conserved Binding Cleft
    A Cavazos, DM Prigozhin, T Alber - Journal of Molecular Biology, 2012 - Elsevier
     
    2. Solution structure of CyanoP from Synechocystis sp. PCC 6803: New insights on the structural basis for functional specialization amongst PsbP family proteins
    SA Jackson, MG Hinds, JJ Eaton-Rye - Biochimica et Biophysica Acta (BBA , 2012 - Elsevier
     

    Protein Summary

    I have built an N- and C-term from this; the families are quite small and do not overlap with anything. There are no sensible hits which might inform on function in either family, so they will end up as DUFs.

     

    More sensitive analysis (by FFAS and HHpred) suggests that the N-terminal domain of BT_1490 is distantly related to the DUF1795/PsbP/Lpp-LpqN (i.e. PF08786/PF01789/PF10738 group of families, which form an unrecognized clan).

     

    The crystal structure of Bacteriodes thetaiotaomicron protein BT_1490 (target DB id 396688, JCSG target ID GE15679B, Genebank accession number NP_810393.1) has been determined to a resolution of 1.5 Angstroms using two-wavelength Se-multiwavelength anomalous disperson. The crystal structure shows that the protein consists of two domains, both with only limited structural similarity to known folds. Crystal packing suggests that a monomer is a significant oligomerization state in solution. BT_1490 protein belongs to a new protein family of about 40 proteins from human gut and marine Bacteroidetes and gamma proteobacteria (Saccharophagus degradans, Congregibacter litoralis) and marine metagenomics datasets. The BT_1490 the structure shows significant novelty, with a never previusly seen combination of two domains, both of which are very divergent variants of previously known folds, detectable only by structure comparison. A gene neighborhood search using the amino acid sequence of BT_1490 shows that in two related species, Bacteroides thetaiotaomicron and Bacteroides vulgatus it lies immediately upstream from a putative ATP binding component of an ATP transporter and a putative histidinol phosphatase.

     

     

     Shown below is a ribbon representation for the monomer of target id 396688 color coded so that the N-terminal region is in blue and the C-terminal region is in red. There are two domains, an N-terminal (residues 1-135)  domain and a C-terminal domain (residues  140-268). A five residue segment connects the two domains. An initial search of structural databases, including FATCAT, indicates that target id 396688 most likely represents the first example of a structure containing this combination of two domains.

     

    monomer_ribbons (2).png

     

     N-Terminal Domain

    The fold N-terminal domain of target id 396688 consists primarily of a seven-stranded anti-parallel beta-sheet with one edge of The N-terminal domain is composed of a beta sheet surrounded by an alpha helix. A second alpha helix forms a bridge across one face of the beta sheet. A search of structural databases using the coordinates of the N-terminal domain of target id 396688 indicates that this domain can be classified as a member of the Mog1p/PsbP-like SCOP superfamily. The results of a DALI search using the coordinates for the N-terminal domain of target id 396688 is tabulated below.

     

    PDB ID Z-Score LALGN rmsd (Ang) %Seq ID Description
    1EQ6 9.6 119 3.3 8 THE SACCHAROMYCES CEREVISIAE RAN-BINDING PROTEIN MOG1P
    1JHS 9.5 117 3.2 9 Protein Mog1 E65A mutant
    1V2B 9.1 117 3.1 13 PsbP Protein in the Oxygen-Evolving Complex of Photosystem II from Higher Plants
    1TU1 7.9 103 3.8 13 Protein of Unknown Function PA94 from Pseudomonas aeruginosa, Putative Regulator
    2I8G 7.4 105 3.9 6 Protein of Unknown Function DIP2269 from Corynebacterium diphtheriae
    1LN2 6.7 96 4.1 8 Human Phosphatidylcholine Transfer Protein in Complex with Dilinoleoylphosphatidylcholine
    1VR8 6.4 83 2.8 5 GTP binding regulator (TM1622) from Thermotoga Maritima at 1.75 A resolution (Pubmed ID 16948158)
    2P4B 6.1 77 3.4 9 Crystal structure of E.coli RseB
    2V42 5.8 78 3.1 9 RSEB: A SENSOR FOR PERIPLASMIC STRESS RESPONSE IN E. COLI

     

    The relatively small degree sequence ID between the N-terminal domain of target ID 396688 and these related structures does not directly indicate a functional role. However, by incorporating two twists, FATCAT analysis on the coordinates of the N-terminal domain of target ID 396688 shows that this N-terminal domain and PDB ID 1TU1,a putative regulator of unknown function from Pseudomonas aeruginoas), can be superimposed with an rmsd of 3.1 Angstroms for 126 aligned residues.  Shown below is a ribbon representation of this FATCAT alignment with the N-terminal domain of target ID 396688 in blue and PDB ID 1TU1 in yellow.

    N_term_domain_versus_1tu1.png

     

    C-Terminal Domain

    A preliminary search of the structural databases using the coordinates of C-terminal domain (residues 140-268) of target ID 396688 indicates that this domain shows some structural novelty. A DALI search reveals that sub-regions of the C-terminal domain are structurally similar to specific regions of the N-terminal domain of the Cre-specific recombinase expressed in E.coli (see Pubmed ID 11340053, Pubmed ID 16756503 for reviews ). Shown below is a superpositioning of the structures of residues 1-130 from the N-terminal domain of PDB ID 1ma7 (yellow) and the C-terminal domain (blue) residues 140-268 of target id 396688. Only three alpha-helices from each domain superimpose.For the alignement shown here, 71 residues are superimposed with an rmsd of 2.9 and 6% sequence identity.

    C_term_align_versus_1ma7.png

    Ligand Summary

    Reviews

    References

     

    No references found.

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